This project will study 206 veterans with Gulf War Illness (GWI) whose symptoms include chronic pain. The first aspect of this study will evaluate a series of Gulf War One (GW1) veterans to identify individuals with these symptoms which in addition to chronic pain may include respiratory difficulty, gastrointestinal problems, dermatologic problems, chronic fatigue, depression, substance abuse, anxiety, cognitive problems and post- traumatic stress disorder (PTSD). Following screening to determine eligibility and informed consent, veterans will be randomly assigned to treatment or sham (placebo) for the study. Additional examinations will compare brain imaging (PET-FDG) across participants. Also, genetic data will be gathered for a pilot sub-study analysis that examines the PON1 gene relationship with GWI symptomatology To determine whether repetitive Transcranial Magnetic Stimulation (rTMS) can be effective in treating the symptoms of chronic pain among veterans with GWI, this project will evaluate the efficacy, safety, durability of benefits and cost-effectiveness of rTMS in the rehabilitation of Veterans with chronic pain in the context of multiple GWI symptoms. We will specifically compare 103 patients receiving rTMS with 103 sham treated patients. Care will be taken to account for common conditions associated with GWI, including fatigue, gastrointestinal problems, dermatologic problems, respiratory problems, cognitive dysfunction, depression, anxiety disorders, substance abuse, and PTSD. It is the intent of this study to determine if the newly FDA-approved treatment for depression, rTMS, may have some benefit to patients with GWS. The data from this study could be used to justify further research in this area.